Microbial navigation and ecology in flow networks

Bacteria often thrive in flow networks, including branched microchannels, vascular systems, tissues, foams, and porous media. Instead of being advected downstream, microbes can swim upstream to reach nutrient sources and colonize favorable habitats. Here, we study experimentally and theoretically how bacteria navigate in these structured environments and actively construct niches surrounded by flows. First, we nanofabricated microfluidic networks with branching and looping architectures. Subsequently, we inoculated these devices with E. coli bacteria and mapped out their dynamics using single-cell tracking. We reveal that bacteria accumulate in specific areas of the network, governed by the currents in the surrounding network segments. By tuning these currents using flow network theory, we can control the bacterial motion and guide their population dynamics. Finally, we explore the ecology of multiple bacterial species in these flow networks and reveal how different architectures affect microbial coexistence, cooperation, and competition. Hence, we achieve programmable control for various functions, including species-specific depletion and accumulation, species sorting, structured community biofilm formation, and biomedical contamination prevention.